101
|
Bertozzi TM, Becker JL, Blake GET, Bansal A, Nguyen DK, Fernandez-Twinn DS, Ozanne SE, Bartolomei MS, Simmons RA, Watson ED, Ferguson-Smith AC. Variably methylated retrotransposons are refractory to a range of environmental perturbations. Nat Genet 2021; 53:1233-1242. [PMID: 34326545 PMCID: PMC7611517 DOI: 10.1038/s41588-021-00898-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/18/2021] [Indexed: 12/27/2022]
Abstract
The agouti viable yellow (Avy) allele is an insertional mutation in the mouse genome caused by a variably methylated intracisternal A particle (VM-IAP) retrotransposon. Avy expressivity is sensitive to a range of early-life chemical exposures and nutritional interventions, suggesting that environmental perturbations can have long-lasting effects on the methylome. However, the extent to which VM-IAP elements are environmentally labile with phenotypic implications is unknown. Using a recently identified repertoire of VM-IAPs, we assessed the epigenetic effects of different environmental contexts. A longitudinal aging analysis indicated that VM-IAPs are stable across the murine lifespan, with only small increases in DNA methylation detected for a subset of loci. No significant effects were observed after maternal exposure to the endocrine disruptor bisphenol A, an obesogenic diet or methyl donor supplementation. A genetic mouse model of abnormal folate metabolism exhibited shifted VM-IAP methylation levels and altered VM-IAP-associated gene expression, yet these effects are likely largely driven by differential targeting by polymorphic KRAB zinc finger proteins. We conclude that epigenetic variability at retrotransposons is not predictive of environmental susceptibility.
Collapse
Affiliation(s)
| | | | - Georgina E T Blake
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Amita Bansal
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Australian National University Medical School, John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Duy K Nguyen
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Denise S Fernandez-Twinn
- University of Cambridge Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust Medical Research Council Institute of Metabolic Science, Cambridge, UK
| | - Susan E Ozanne
- University of Cambridge Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust Medical Research Council Institute of Metabolic Science, Cambridge, UK
| | - Marisa S Bartolomei
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca A Simmons
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erica D Watson
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
| |
Collapse
|
102
|
Xia X, Wang Y, Yu Z, Chen J, Han JDJ. Assessing the rate of aging to monitor aging itself. Ageing Res Rev 2021; 69:101350. [PMID: 33940202 DOI: 10.1016/j.arr.2021.101350] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 04/05/2021] [Accepted: 04/26/2021] [Indexed: 12/22/2022]
Abstract
Healthy aging is the prime goal of aging research and interventions. Healthy aging or not can be quantified by biological aging rates estimated by aging clocks. Generation and accumulation of large scale high-dimensional biological data together with maturation of artificial intelligence among other machine learning techniques, have enabled and spurred the rapid development of various aging rate estimators (aging clocks). Here we review the data sources and compare the algorithms of recent human aging clocks, and the applications of these clocks in both researches and daily life. We envision that not only more and multiscale data on cross-sectional data will add momentum to the aging clock development, new longitudinal and interventional data will further raise the aging clock development to the next level to be trained by true biological age such as morbidity and mortality age.
Collapse
|
103
|
Li Y, Zhou LQ. dCas9 techniques for transcriptional repression in mammalian cells: Progress, applications and challenges. Bioessays 2021; 43:e2100086. [PMID: 34327721 DOI: 10.1002/bies.202100086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/10/2023]
Abstract
Innovative loss-of-function techniques developed in recent years have made it much easier to target specific genomic loci at transcriptional levels. CRISPR interference (CRISPRi) has been proven to be the most effective and specific tool to knock down any gene of interest in mammalian cells. The catalytically deactivated Cas9 (dCas9) can be fused with transcription repressors to downregulate gene expression specified by sgRNA complementary to target genomic sequence. Although CRISPRi has huge potential for gene knockdown, there is still a lack of systematic guidelines for efficient and widespread use. Here we describe the working mechanism and development of CRISPRi, designing principles of sgRNA, delivery methods and applications in mammalian cells in detail. Finally, we propose possible solutions and future directions with regard to current challenges.
Collapse
Affiliation(s)
- Yuanyuan Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
104
|
Sugrue VJ, Zoller JA, Narayan P, Lu AT, Ortega-Recalde OJ, Grant MJ, Bawden CS, Rudiger SR, Haghani A, Bond DM, Hore RR, Garratt M, Sears KE, Wang N, Yang XW, Snell RG, Hore TA, Horvath S. Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci. eLife 2021; 10:e64932. [PMID: 34227937 PMCID: PMC8260231 DOI: 10.7554/elife.64932] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/15/2021] [Indexed: 12/26/2022] Open
Abstract
In mammals, females generally live longer than males. Nevertheless, the mechanisms underpinning sex-dependent longevity are currently unclear. Epigenetic clocks are powerful biological biomarkers capable of precisely estimating chronological age and identifying novel factors influencing the aging rate using only DNA methylation data. In this study, we developed the first epigenetic clock for domesticated sheep (Ovis aries), which can predict chronological age with a median absolute error of 5.1 months. We have discovered that castrated male sheep have a decelerated aging rate compared to intact males, mediated at least in part by the removal of androgens. Furthermore, we identified several androgen-sensitive CpG dinucleotides that become progressively hypomethylated with age in intact males, but remain stable in castrated males and females. Comparable sex-specific methylation differences in MKLN1 also exist in bat skin and a range of mouse tissues that have high androgen receptor expression, indicating that it may drive androgen-dependent hypomethylation in divergent mammalian species. In characterizing these sites, we identify biologically plausible mechanisms explaining how androgens drive male-accelerated aging.
Collapse
Affiliation(s)
| | - Joseph Alan Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los AngelesLos AngelesUnited States
| | - Pritika Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of AucklandAucklandNew Zealand
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | | | - Matthew J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of AucklandAucklandNew Zealand
| | - C Simon Bawden
- Livestock and Farming Systems, South Australian Research and Development InstituteRoseworthyAustralia
| | - Skye R Rudiger
- Livestock and Farming Systems, South Australian Research and Development InstituteRoseworthyAustralia
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Donna M Bond
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Reuben R Hore
- Blackstone Hill Station, Becks, RD2OmakauNew Zealand
| | - Michael Garratt
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, UCLALos AngelesUnited States
| | - Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles (UCLA)Los AngelesUnited States
| | - Xiangdong William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles (UCLA)Los AngelesUnited States
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLALos AngelesUnited States
| | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of AucklandAucklandNew Zealand
| | - Timothy A Hore
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| |
Collapse
|
105
|
Zupkovitz G, Kabiljo J, Kothmayer M, Schlick K, Schöfer C, Lagger S, Pusch O. Analysis of Methylation Dynamics Reveals a Tissue-Specific, Age-Dependent Decline in 5-Methylcytosine Within the Genome of the Vertebrate Aging Model Nothobranchius furzeri. Front Mol Biosci 2021; 8:627143. [PMID: 34222326 PMCID: PMC8242171 DOI: 10.3389/fmolb.2021.627143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
Erosion of the epigenetic DNA methylation landscape is a widely recognized hallmark of aging. Emerging advances in high throughput sequencing techniques, in particular DNA methylation data analysis, have resulted in the establishment of precise human and murine age prediction tools. In vertebrates, methylation of cytosine at the C5 position of CpG dinucleotides is executed by DNA methyltransferases (DNMTs) whereas the process of enzymatic demethylation is highly dependent on the activity of the ten-eleven translocation methylcytosine dioxygenase (TET) family of enzymes. Here, we report the identification of the key players constituting the DNA methylation machinery in the short-lived teleost aging model Nothobranchius furzeri. We present a comprehensive spatio-temporal expression profile of the methylation-associated enzymes from embryogenesis into late adulthood, thereby covering the complete killifish life cycle. Data mining of the N. furzeri genome produced five dnmt gene family orthologues corresponding to the mammalian DNMTs (DNMT1, 2, 3A, and 3B). Comparable to other teleost species, N. furzeri harbors multiple genomic copies of the de novo DNA methylation subfamily. A related search for the DNMT1 recruitment factor UHRF1 and TET family members resulted in the identification of N. furzeri uhrf1, tet1, tet2, and tet3. Phylogenetic analysis revealed high cross-species similarity on the amino acid level of all individual dnmts, tets, and uhrf1, emphasizing a high degree of functional conservation. During early killifish development all analyzed dnmts and tets showed a similar expression profile characterized by a strong increase in transcript levels after fertilization, peaking either at embryonic day 6 or at the black eye stage of embryonic development. In adult N. furzeri, DNA methylation regulating enzymes showed a ubiquitous tissue distribution. Specifically, we observed an age-dependent downregulation of dnmts, and to some extent uhrf1, which correlated with a significant decrease in global DNA methylation levels in the aging killifish liver and muscle. The age-dependent DNA methylation profile and spatio-temporal expression characteristics of its enzymatic machinery reported here may serve as an essential platform for the identification of an epigenetic aging clock in the new vertebrate model system N. furzeri.
Collapse
Affiliation(s)
- Gordin Zupkovitz
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.,Department of Life Science Engineering, University of Applied Sciences Technikum Wien, Vienna, Austria.,City of Vienna Competence Team Aging Tissue, Vienna, Austria
| | - Julijan Kabiljo
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.,Department of General Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Michael Kothmayer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Katharina Schlick
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Christian Schöfer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sabine Lagger
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Oliver Pusch
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
106
|
Kerepesi C, Zhang B, Lee SG, Trapp A, Gladyshev VN. Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging. SCIENCE ADVANCES 2021; 7:eabg6082. [PMID: 34172448 PMCID: PMC8232908 DOI: 10.1126/sciadv.abg6082] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
The notion that the germ line does not age goes back to the 19th-century ideas of August Weismann. However, being metabolically active, the germ line accumulates damage and other changes over time, i.e., it ages. For new life to begin in the same young state, the germ line must be rejuvenated in the offspring. Here, we developed a multi-tissue epigenetic clock and applied it, together with other aging clocks, to track changes in biological age during mouse and human prenatal development. This analysis revealed a significant decrease in biological age, i.e., rejuvenation, during early stages of embryogenesis, followed by an increase in later stages. We further found that pluripotent stem cells do not age even after extensive passaging and that the examined epigenetic age dynamics is conserved across species. Overall, this study uncovers a natural rejuvenation event during embryogenesis and suggests that the minimal biological age (ground zero) marks the beginning of organismal aging.
Collapse
Affiliation(s)
- Csaba Kerepesi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexandre Trapp
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
107
|
Robeck TR, Fei Z, Lu AT, Haghani A, Jourdain E, Zoller JA, Li CZ, Steinman KJ, DiRocco S, Schmitt T, Osborn S, Van Bonn B, Katsumata E, Mergl J, Almunia J, Rodriguez M, Haulena M, Dold C, Horvath S. Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins. Commun Biol 2021; 4:642. [PMID: 34059764 PMCID: PMC8167141 DOI: 10.1038/s42003-021-02179-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
The development of a precise blood or skin tissue DNA Epigenetic Aging Clock for Odontocete (OEAC) would solve current age estimation inaccuracies for wild odontocetes. Therefore, we determined genome-wide DNA methylation profiles using a custom array (HorvathMammalMethyl40) across skin and blood samples (n = 446) from known age animals representing nine odontocete species within 4 phylogenetic families to identify age associated CG dinucleotides (CpGs). The top CpGs were used to create a cross-validated OEAC clock which was highly correlated for individuals (r = 0.94) and for unique species (median r = 0.93). Finally, we applied the OEAC for estimating the age and sex of 22 wild Norwegian killer whales. DNA methylation patterns of age associated CpGs are highly conserved across odontocetes. These similarities allowed us to develop an odontocete epigenetic aging clock (OEAC) which can be used for species conservation efforts by provide a mechanism for estimating the age of free ranging odontocetes from either blood or skin samples.
Collapse
Affiliation(s)
- Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA.
| | - Zhe Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Caesar Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karen J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | | | | | | | | | | | - June Mergl
- Marineland of Canada, Niagara Falls, ON, Canada
| | - Javier Almunia
- Loro Parque Fundación, SA, Avenida Loro Parque, Puerto de la Cruz, Santa Cruz de Tenerife, Spain
| | | | | | - Christopher Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
108
|
Mayne B, Berry O, Jarman S. Optimal sample size for calibrating DNA methylation age estimators. Mol Ecol Resour 2021; 21:2316-2323. [PMID: 34053192 PMCID: PMC8518423 DOI: 10.1111/1755-0998.13437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
Age is a fundamental parameter in wildlife management as it is used to determine the risk of extinction, manage invasive species, and regulate sustainable harvest. In a broad variety of vertebrates species, age can be determined by measuring DNA methylation. Animals with known ages are initially required during development, calibration, and validation of these epigenetic clocks. However, wild animals with known ages are frequently difficult to obtain. Here, we perform Monte‐Carlo simulations to determine the optimal sample size required to create an accurate calibration model for age estimation by elastic net regression modelling of cytosine‐phosphate‐guanine methylation data. Our results suggest a minimum calibration population size of 70, but ideally 134 individuals or more for accurate and precise models. We also provide estimates to the extent a model can be extrapolated beyond a distribution of ages that was used during calibration. The findings can assist researchers to better design age estimation models and decide if their model is adequate for determining key population attributes.
Collapse
Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Simon Jarman
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| |
Collapse
|
109
|
Chen Z, Stanbouly S, Nishiyama NC, Chen X, Delp MD, Qiu H, Mao XW, Wang C. Spaceflight decelerates the epigenetic clock orchestrated with a global alteration in DNA methylome and transcriptome in the mouse retina. PRECISION CLINICAL MEDICINE 2021; 4:93-108. [PMID: 34179686 PMCID: PMC8220224 DOI: 10.1093/pcmedi/pbab012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/27/2021] [Accepted: 05/13/2021] [Indexed: 01/30/2023] Open
Abstract
Astronauts exhibit an assortment of clinical abnormalities in their eyes during long-duration spaceflight. The purpose of this study was to determine whether spaceflight induces epigenomic and transcriptomic reprogramming in the retina or alters the epigenetic clock. The mice were flown for 37 days in animal enclosure modules on the International Space Station; ground-based control animals were maintained under similar housing conditions. Mouse retinas were isolated and both DNA methylome and transcriptome were determined by deep sequencing. We found that a large number of genes were differentially methylated with spaceflight, whereas there were fewer differentially expressed genes at the transcriptome level. Several biological pathways involved in retinal diseases such as macular degeneration were significantly altered. Our results indicated that spaceflight decelerated the retinal epigenetic clock. This study demonstrates that spaceflight impacts the retina at the epigenomic and transcriptomic levels, and such changes could be involved in the etiology of eye-related disorders among astronauts.
Collapse
Affiliation(s)
- Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Seta Stanbouly
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Nina C Nishiyama
- Division of Radiation Research, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Xin Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Michael D Delp
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, FL 32306, USA
| | - Hongyu Qiu
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA
| | - Xiao W Mao
- Division of Radiation Research, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| |
Collapse
|
110
|
Acton RJ, Yuan W, Gao F, Xia Y, Bourne E, Wozniak E, Bell J, Lillycrop K, Wang J, Dennison E, Harvey NC, Mein CA, Spector TD, Hysi PG, Cooper C, Bell CG. The genomic loci of specific human tRNA genes exhibit ageing-related DNA hypermethylation. Nat Commun 2021; 12:2655. [PMID: 33976121 PMCID: PMC8113476 DOI: 10.1038/s41467-021-22639-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/05/2021] [Indexed: 02/03/2023] Open
Abstract
The epigenome has been shown to deteriorate with age, potentially impacting on ageing-related disease. tRNA, while arising from only ˜46 kb (<0.002% genome), is the second most abundant cellular transcript. tRNAs also control metabolic processes known to affect ageing, through core translational and additional regulatory roles. Here, we interrogate the DNA methylation state of the genomic loci of human tRNA. We identify a genomic enrichment for age-related DNA hypermethylation at tRNA loci. Analysis in 4,350 MeDIP-seq peripheral-blood DNA methylomes (16-82 years), identifies 44 and 21 hypermethylating specific tRNAs at study-and genome-wide significance, respectively, contrasting with none hypomethylating. Validation and replication (450k array and independent targeted Bisuphite-sequencing) supported the hypermethylation of this functional unit. Tissue-specificity is a significant driver, although the strongest consistent signals, also independent of major cell-type change, occur in tRNA-iMet-CAT-1-4 and tRNA-Ser-AGA-2-6. This study presents a comprehensive evaluation of the genomic DNA methylation state of human tRNA genes and reveals a discreet hypermethylation with advancing age.
Collapse
Affiliation(s)
- Richard J Acton
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Charterhouse Square, Queen Mary University of London, London, UK
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Wei Yuan
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
- Institute of Cancer Research, Sutton, UK
| | - Fei Gao
- BGI-Shenzhen, Shenzhen, China
| | | | - Emma Bourne
- Barts & The London Genome Centre, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eva Wozniak
- Barts & The London Genome Centre, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jordana Bell
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
| | - Karen Lillycrop
- Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Jun Wang
- Shenzhen Digital Life Institute, Shenzhen, Guangdong, China
- iCarbonX, Zhuhai, Guangdong, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China
| | - Elaine Dennison
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Charles A Mein
- Barts & The London Genome Centre, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Christopher G Bell
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Charterhouse Square, Queen Mary University of London, London, UK.
| |
Collapse
|
111
|
Costa Dos Santos G, Renovato-Martins M, de Brito NM. The remodel of the "central dogma": a metabolomics interaction perspective. Metabolomics 2021; 17:48. [PMID: 33969452 PMCID: PMC8106972 DOI: 10.1007/s11306-021-01800-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND In 1957, Francis Crick drew a linear diagram on a blackboard. This diagram is often called the "central dogma." Subsequently, the relationships between different steps of the "central dogma" have been shown to be considerably complex, mostly because of the emerging world of small molecules. It is noteworthy that metabolites can be generated from the diet through gut microbiome metabolism, serve as substrates for epigenetic modifications, destabilize DNA quadruplexes, and follow Lamarckian inheritance. Small molecules were once considered the missing link in the "central dogma"; however, recently they have acquired a central role, and their general perception as downstream products has become reductionist. Metabolomics is a large-scale analysis of metabolites, and this emerging field has been shown to be the closest omics associated with the phenotype and concomitantly, the basis for all omics. AIM OF REVIEW Herein, we propose a broad updated perspective for the flux of information diagram centered in metabolomics, including the influence of other factors, such as epigenomics, diet, nutrition, and the gut- microbiome. KEY SCIENTIFIC CONCEPTS OF REVIEW Metabolites are the beginning and the end of the flux of information.
Collapse
Affiliation(s)
- Gilson Costa Dos Santos
- Laboratory of NMR Metabolomics, IBRAG, Department of Genetics, State University of Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil.
| | - Mariana Renovato-Martins
- Department of Cellular and Molecular Biology, IB, Federal Fluminense University, Niterói, 24210-200, Brazil
| | - Natália Mesquita de Brito
- Laboratory of Cellular and Molecular Pharmacology, IBRAG, Department of Cell Biology, State University of Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil.
| |
Collapse
|
112
|
Kordowitzki P, Haghani A, Zoller JA, Li CZ, Raj K, Spangler ML, Horvath S. Epigenetic clock and methylation study of oocytes from a bovine model of reproductive aging. Aging Cell 2021; 20:e13349. [PMID: 33797841 PMCID: PMC8135012 DOI: 10.1111/acel.13349] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/05/2021] [Accepted: 03/07/2021] [Indexed: 12/24/2022] Open
Abstract
Cattle are an attractive animal model of fertility in women due to their high degree of similarity relative to follicle selection, embryo cleavage, blastocyst formation, and gestation length. To facilitate future studies of the epigenetic underpinnings of aging effects in the female reproductive axis, several DNA methylation-based biomarkers of aging (epigenetic clocks) for bovine oocytes are presented. One such clock was germane to only oocytes, while a dual-tissue clock was highly predictive of age in both oocytes and blood. Dual species clocks that apply to both humans and cattle were also developed and evaluated. These epigenetic clocks can be used to accurately estimate the biological age of oocytes. Both epigenetic clock studies and epigenome-wide association studies revealed that blood and oocytes differ substantially with respect to aging and the underlying epigenetic signatures that potentially influence the aging process. The rate of epigenetic aging was found to be slower in oocytes compared to blood; however, oocytes appeared to begin at an older epigenetic age. The epigenetic clocks for oocytes are expected to address questions in the field of reproductive aging, including the central question: how to slow aging of oocytes.
Collapse
Affiliation(s)
- Paweł Kordowitzki
- Institute of Animal Reproduction and Food Research of Polish Academy of SciencesOlsztynPoland
- Institute for Veterinary MedicineNicolaus Copernicus UniversityTorunPoland
| | - Amin Haghani
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Joseph A. Zoller
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
| | - Caesar Z. Li
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
| | - Ken Raj
- Radiation Effects DepartmentCentre for Radiation, Chemical and Environmental HazardsPublic Health EnglandDidcotUK
| | | | - Steve Horvath
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
| |
Collapse
|
113
|
Bors EK, Baker CS, Wade PR, O'Neill KB, Shelden KEW, Thompson MJ, Fei Z, Jarman S, Horvath S. An epigenetic clock to estimate the age of living beluga whales. Evol Appl 2021; 14:1263-1273. [PMID: 34025766 PMCID: PMC8127720 DOI: 10.1111/eva.13195] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
DNA methylation data facilitate the development of accurate molecular estimators of chronological age or "epigenetic clocks." We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. We used a custom methylation array to measure methylation levels at 37,491 cytosine-guanine sites (CpGs) from skin samples of dead whales (n = 67) whose chronological ages were estimated based on tooth growth layer groups. Using these calibration data, a penalized regression model selected 23 CpGs, providing an R 2 = 0.92 for the training data; and an R 2 = 0.74 and median absolute age error = 2.9 years for the leave one out cross-validation. We applied the epigenetic clock to an independent dataset of 38 skin samples collected with a biopsy dart from living whales between 2016 and 2018. Age estimates ranged from 11 to 27 years. We also report sex correlations in CpG data and describe an approach of identifying the sex of an animal using DNA methylation. The epigenetic estimators of age and sex presented here have broad applications for conservation and management of Cook Inlet beluga whales and potentially other cetaceans.
Collapse
Affiliation(s)
| | - C. Scott Baker
- Marine Mammal InstituteOregon State UniversityNewportORUSA
| | - Paul R. Wade
- Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanographic and Atmospheric AdministrationSeattleWAUSA
| | | | - Kim E. W. Shelden
- Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanographic and Atmospheric AdministrationSeattleWAUSA
| | - Michael J. Thompson
- Molecular, Cell and Developmental BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | - Zhe Fei
- Department of BiostatisticsSchool of Public HealthUniversity of California‐Los AngelesLos AngelesCAUSA
| | - Simon Jarman
- School of Biological SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Steve Horvath
- Department of BiostatisticsSchool of Public HealthUniversity of California‐Los AngelesLos AngelesCAUSA
- Department of Human GeneticsGonda Research CenterDavid Geffen School of MedicineLos AngelesCAUSA
| |
Collapse
|
114
|
Larocca D, Lee J, West MD, Labat I, Sternberg H. No Time to Age: Uncoupling Aging from Chronological Time. Genes (Basel) 2021; 12:611. [PMID: 33919082 PMCID: PMC8143125 DOI: 10.3390/genes12050611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
Multicellular life evolved from simple unicellular organisms that could replicate indefinitely, being essentially ageless. At this point, life split into two fundamentally different cell types: the immortal germline representing an unbroken lineage of cell division with no intrinsic endpoint and the mortal soma, which ages and dies. In this review, we describe the germline as clock-free and the soma as clock-bound and discuss aging with respect to three DNA-based cellular clocks (telomeric, DNA methylation, and transposable element). The ticking of these clocks corresponds to the stepwise progressive limitation of growth and regeneration of somatic cells that we term somatic restriction. Somatic restriction acts in opposition to strategies that ensure continued germline replication and regeneration. We thus consider the plasticity of aging as a process not fixed to the pace of chronological time but one that can speed up or slow down depending on the rate of intrinsic cellular clocks. We further describe how germline factor reprogramming might be used to slow the rate of aging and potentially reverse it by causing the clocks to tick backward. Therefore, reprogramming may eventually lead to therapeutic strategies to treat degenerative diseases by altering aging itself, the one condition common to us all.
Collapse
Affiliation(s)
| | - Jieun Lee
- AgeX Therapeutics Inc., Alameda, CA 94501, USA; (J.L.); (M.D.W.); (I.L.); (H.S.)
| | - Michael D. West
- AgeX Therapeutics Inc., Alameda, CA 94501, USA; (J.L.); (M.D.W.); (I.L.); (H.S.)
| | - Ivan Labat
- AgeX Therapeutics Inc., Alameda, CA 94501, USA; (J.L.); (M.D.W.); (I.L.); (H.S.)
| | - Hal Sternberg
- AgeX Therapeutics Inc., Alameda, CA 94501, USA; (J.L.); (M.D.W.); (I.L.); (H.S.)
| |
Collapse
|
115
|
Zhang MJ, Pisco AO, Darmanis S, Zou J. Mouse aging cell atlas analysis reveals global and cell type-specific aging signatures. eLife 2021; 10:62293. [PMID: 33847263 PMCID: PMC8046488 DOI: 10.7554/elife.62293] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/29/2021] [Indexed: 12/15/2022] Open
Abstract
Aging is associated with complex molecular and cellular processes that are poorly understood. Here we leveraged the Tabula Muris Senis single-cell RNA-seq data set to systematically characterize gene expression changes during aging across diverse cell types in the mouse. We identified aging-dependent genes in 76 tissue-cell types from 23 tissues and characterized both shared and tissue-cell-specific aging behaviors. We found that the aging-related genes shared by multiple tissue-cell types also change their expression congruently in the same direction during aging in most tissue-cell types, suggesting a coordinated global aging behavior at the organismal level. Scoring cells based on these shared aging genes allowed us to contrast the aging status of different tissues and cell types from a transcriptomic perspective. In addition, we identified genes that exhibit age-related expression changes specific to each functional category of tissue-cell types. Altogether, our analyses provide one of the most comprehensive and systematic characterizations of the molecular signatures of aging across diverse tissue-cell types in a mammalian system.
Collapse
Affiliation(s)
- Martin Jinye Zhang
- Department of Electrical Engineering, Stanford University, Palo Alto, United States.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, United States.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, United States
| | | | | | - James Zou
- Department of Electrical Engineering, Stanford University, Palo Alto, United States.,Chan-Zuckerberg Biohub, San Francisco, United States.,Department of Biomedical Data Science, Stanford University, Palo Alto, United States
| |
Collapse
|
116
|
Roudbar MA, Mousavi SF, Ardestani SS, Lopes FB, Momen M, Gianola D, Khatib H. Prediction of biological age and evaluation of genome-wide dynamic methylomic changes throughout human aging. G3-GENES GENOMES GENETICS 2021; 11:6214518. [PMID: 33826720 PMCID: PMC8495934 DOI: 10.1093/g3journal/jkab112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/29/2021] [Indexed: 11/14/2022]
Abstract
The use of DNA methylation signatures to predict chronological age and aging rate is of interest in many fields, including disease prevention and treatment, forensics, and anti-aging medicine. Although a large number of methylation markers are significantly associated with age, most age-prediction methods use a few markers selected based on either previously published studies or datasets containing methylation information. Here, we implemented reproducing kernel Hilbert spaces (RKHS) regression and a ridge regression model in a Bayesian framework that utilized phenotypic and methylation profiles simultaneously to predict chronological age. We used over 450,000 CpG sites from the whole blood of a large cohort of 4,409 human individuals with a range of 10-101 years of age. Models were fitted using adjusted and un-adjusted methylation measurements for cell heterogeneity. Un-adjusted methylation scores delivered a significantly higher prediction accuracy than adjusted methylation data, with a correlation between age and predicted age of 0.98 and a root-mean-square error (RMSE) of 3.54 years in un-adjusted data, and 0.90 (correlation) and 7.16 (RMSE) years in adjusted data. Reducing the number of predictors (CpG sites) through subset selection improved predictive power with a correlation of 0.98 and an RMSE of 2.98 years in the RKHS model. We found distinct global methylation patterns, with a significant increase in the proportion of methylated cytosines in CpG islands and a decreased proportion in other CpG types, including CpG shore, shelf, and open sea (p < 5e-06). Epigenetic drift seemed to be a widespread phenomenon as more than 97% of the age-associated methylation sites had heteroscedasticity. Apparent methylomic aging rate (AMAR) had a sex-specific pattern, with an increase in AMAR in females with age related to males.
Collapse
Affiliation(s)
- Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Dezful, Iran
| | - Seyedeh Fatemeh Mousavi
- Department of Animal Science, Faculty of Agriculture Engineering, University of Kurdistan, Sanandaj, Iran
| | - Siavash Salek Ardestani
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Fernando Brito Lopes
- Department of Animal Sciences, Sao Paulo State University, Julio de Mesquita Filho (UNESP), Prof. Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil
| | - Mehdi Momen
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel Gianola
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 53706, Madison, WI, USA
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 53706, Madison, WI, USA
| |
Collapse
|
117
|
Anderson JA, Johnston RA, Lea AJ, Campos FA, Voyles TN, Akinyi MY, Alberts SC, Archie EA, Tung J. High social status males experience accelerated epigenetic aging in wild baboons. eLife 2021; 10:e66128. [PMID: 33821798 PMCID: PMC8087445 DOI: 10.7554/elife.66128] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/18/2021] [Indexed: 12/14/2022] Open
Abstract
Aging, for virtually all life, is inescapable. However, within populations, biological aging rates vary. Understanding sources of variation in this process is central to understanding the biodemography of natural populations. We constructed a DNA methylation-based age predictor for an intensively studied wild baboon population in Kenya. Consistent with findings in humans, the resulting 'epigenetic clock' closely tracks chronological age, but individuals are predicted to be somewhat older or younger than their known ages. Surprisingly, these deviations are not explained by the strongest predictors of lifespan in this population, early adversity and social integration. Instead, they are best predicted by male dominance rank: high-ranking males are predicted to be older than their true ages, and epigenetic age tracks changes in rank over time. Our results argue that achieving high rank for male baboons - the best predictor of reproductive success - imposes costs consistent with a 'live fast, die young' life-history strategy.
Collapse
Affiliation(s)
- Jordan A Anderson
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Rachel A Johnston
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Amanda J Lea
- Department of Biology, Duke UniversityDurhamUnited States
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton UniversityPrincetonUnited States
- Department of Ecology and Evolution, Princeton UniversityPrincetonUnited States
| | - Fernando A Campos
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Anthropology, University of Texas at San AntonioSan AntonioUnited States
| | - Tawni N Voyles
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Mercy Y Akinyi
- Institute of Primate Research, National Museums of KenyaNairobiKenya
| | - Susan C Alberts
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Department of Biology, Duke UniversityDurhamUnited States
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Department of Biology, Duke UniversityDurhamUnited States
- Duke Population Research Institute, Duke UniversityDurhamUnited States
- Canadian Institute for Advanced ResearchTorontoCanada
| |
Collapse
|
118
|
DNA methylation predicts age and provides insight into exceptional longevity of bats. Nat Commun 2021; 12:1615. [PMID: 33712580 PMCID: PMC7955057 DOI: 10.1038/s41467-021-21900-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/08/2021] [Indexed: 01/31/2023] Open
Abstract
Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.
Collapse
|
119
|
Metabolomic-based clinical studies and murine models for acute pancreatitis disease: A review. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166123. [PMID: 33713791 DOI: 10.1016/j.bbadis.2021.166123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/21/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
Acute pancreatitis (AP) is one of the most common gastroenterological disorders requiring hospitalization and is associated with substantial morbidity and mortality. Metabolomics nowadays not only help us to understand cellular metabolism to a degree that was not previously obtainable, but also to reveal the importance of the metabolites in physiological control, disease onset and development. An in-depth understanding of metabolic phenotyping would be therefore crucial for accurate diagnosis, prognosis and precise treatment of AP. In this review, we summarized and addressed the metabolomics design and workflow in AP studies, as well as the results and analysis of the in-depth of research. Based on the metabolic profiling work in both clinical populations and experimental AP models, we described the metabolites with potential utility as biomarkers and the correlation between the altered metabolites and AP status. Moreover, the disturbed metabolic pathways correlated with biological function were discussed in the end. A practical understanding of current and emerging metabolomic approaches applicable to AP and use of the metabolite information presented will aid in designing robust metabolomics and biological experiments that result in identification of unique biomarkers and mechanisms, and ultimately enhanced clinical decision-making.
Collapse
|
120
|
Abstract
Growth hormone (GH) actions impact growth, metabolism, and body composition and have been associated with aging and longevity. Lack of GH results in slower growth, delayed maturation, and reduced body size and can lead to delayed aging, increased healthspan, and a remarkable extension of longevity. Adult body size, which is a GH-dependent trait, has a negative association with longevity in several mammalian species. Mechanistic links between GH and aging include evolutionarily conserved insulin/insulin-like growth factors and mechanistic target of rapamycin signaling pathways in accordance with long-suspected trade-offs between anabolic/growth processes and longevity. Height and the rate and regulation of GH secretion have been related to human aging, but longevity is not extended in humans with syndromes of GH deficiency or resistance. However, the risk of age-related chronic disease is reduced in individuals affected by these syndromes and various indices of increased healthspan have been reported.
Collapse
Affiliation(s)
- Andrzej Bartke
- Southern Illinois University School of Medicine, 801 N. Rutledge, P.O. Box 19628, Springfield, IL, 62794-9628, USA.
| |
Collapse
|
121
|
Chiavellini P, Canatelli-Mallat M, Lehmann M, Gallardo MD, Herenu CB, Cordeiro JL, Clement J, Goya RG. Aging and rejuvenation - a modular epigenome model. Aging (Albany NY) 2021; 13:4734-4746. [PMID: 33627519 PMCID: PMC7950254 DOI: 10.18632/aging.202712] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/08/2021] [Indexed: 12/21/2022]
Abstract
The view of aging has evolved in parallel with the advances in biomedical sciences. Long considered as an irreversible process where interventions were only aimed at slowing down its progression, breakthrough discoveries like animal cloning and cell reprogramming have deeply changed our understanding of postnatal development, giving rise to the emerging view that the epigenome is the driver of aging. The idea was significantly strengthened by the converging discovery that DNA methylation (DNAm) at specific CpG sites could be used as a highly accurate biomarker of age defined by an algorithm known as the Horvath clock. It was at this point where epigenetic rejuvenation came into play as a strategy to reveal to what extent biological age can be set back by making the clock tick backwards. Initial evidence suggests that when the clock is forced to tick backwards in vivo, it is only able to drag the phenotype to a partially rejuvenated condition. In order to explain the results, a bimodular epigenome is proposed, where module A represents the DNAm clock component and module B the remainder of the epigenome. Epigenetic rejuvenation seems to hold the key to arresting or even reversing organismal aging.
Collapse
Affiliation(s)
- Priscila Chiavellini
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Martina Canatelli-Mallat
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Marianne Lehmann
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Maria D Gallardo
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Claudia B Herenu
- Institute for Experimental Pharmacology (IFEC), School of Chemical Sciences, National University of Cordoba, Cordoba, Argentina
| | - Jose L Cordeiro
- World Academy of Art and Science (WAAS), Napa, CA 94558, USA
| | | | - Rodolfo G Goya
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| |
Collapse
|
122
|
Xiao L, Zan G, Feng X, Bao Y, Huang S, Luo X, Xu X, Zhang Z, Yang X. The associations of multiple metals mixture with accelerated DNA methylation aging. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 269:116230. [PMID: 33316491 DOI: 10.1016/j.envpol.2020.116230] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/29/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Aging is a leading cause of mortality for the elderly and DNA methylation age is reported to be predictive of biological aging. However, few studies have investigated the associations between multiple metals exposure and accelerated aging in the elderly. We performed a pilot study of 288 elderly participants aged 50-115 years and measured genome-wide DNA methylation and 22 blood metals concentrations. Measures of DNA methylation age were estimated using CpGs from Illumina HumanMethylation EPIC BeadChip. Linear mixed regression and Bayesian kernel machine regression (BKMR) models were used to estimate the individual and overall associations between multiple metals and accelerated methylation aging. Single metal models revealed that each 1-standard deviance (SD) increase in log-transformed vanadium, cobalt, nickel, zinc, arsenic, and barium was associated with a -2.256, -1.318, 1.004, -1.926, 1.910 and -1.356 changes in ΔAge, respectively; meanwhile, for aging rate, the change was -0.019, -0.013, 0.010, -0.018, 0.023, and -0.012, respectively (all P < 0.05). The BKMR models showed reverse U-shaped associations of the overall metals mixture with ΔAge and aging rate. Downward trends of ΔAge and aging rate were observed for increasing quantiles of essential metals mixture, but upward trends were observed for non-essential metals mixture. Further individual analysis of the BKMR revealed that the 95% confidence interval of ΔAge and aging rate associated with vanadium, zinc, and arsenic did not cross 0, when other metals concentrations set at 25th, 50th, and 75th percentile. Our findings suggest reverse U-shaped associations of the overall metals mixture with accelerated methylation aging for the first time, and vanadium, zinc, and arsenic may be major contributors driving the associations.
Collapse
Affiliation(s)
- Lili Xiao
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Gaohui Zan
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiuming Feng
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Yu Bao
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Sifang Huang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoyu Luo
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Xia Xu
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Zhiyong Zhang
- School of Public Health, Guilin Medical University, Guilin, Guangxi, China
| | - Xiaobo Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China; Department of Public Health, School of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi, China.
| |
Collapse
|
123
|
Liu S, Wang K, Svoboda LK, Rygiel CA, Neier K, Jones TR, Cavalcante RG, Colacino JA, Dolinoy DC, Sartor MA. Perinatal DEHP exposure induces sex- and tissue-specific DNA methylation changes in both juvenile and adult mice. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab004. [PMID: 33986952 PMCID: PMC8107644 DOI: 10.1093/eep/dvab004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/12/2021] [Accepted: 03/17/2021] [Indexed: 05/04/2023]
Abstract
Di(2-ethylhexyl) phthalate (DEHP) is a type of phthalate plasticizer found in a variety of consumer products and poses a public health concern due to its metabolic and endocrine disruption activities. Dysregulation of epigenetic modifications, including DNA methylation, has been shown to be an important mechanism for the pathogenic effects of prenatal exposures, including phthalates. In this study, we used an established mouse model to study the effect of perinatal DEHP exposure on the DNA methylation profile in liver (a primary target tissue of DEHP) and blood (a common surrogate tissue) of both juvenile and adult mice. Despite exposure ceasing at 3 weeks of age (PND21), we identified thousands of sex-specific differential DNA methylation events in 5-month old mice, more than identified at PND21, both in blood and liver. Only a small number of these differentially methylated cytosines (DMCs) overlapped between the time points, or between tissues (i.e. liver and blood), indicating blood may not be an appropriate surrogate tissue to estimate the effects of DEHP exposure on liver DNA methylation. We detected sex-specific DMCs common between 3-week and 5-month samples, pointing to specific DNA methylation alterations that are consistent between weanling and adult mice. In summary, this is the first study to assess the genome-wide DNA methylation profiles in liver and blood at two different aged cohorts in response to perinatal DEHP exposure. Our findings cast light on the implications of using surrogate tissue instead of target tissue in human population-based studies and identify epigenetic biomarkers for DEHP exposure.
Collapse
Affiliation(s)
- Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Laurie K Svoboda
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Christine A Rygiel
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Kari Neier
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Tamara R Jones
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Raymond G Cavalcante
- Epigenomics Core, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Justin A Colacino
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Dana C Dolinoy
- Correspondence address. Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, USA. Tel: +734-647-3155; Fax: +734-936-7283; E-mail: (D.C.D.); Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI 48109-2218, USA . Tel: +734-763-8013; Fax: +734-615-6553; E-mail: (M.A.S.)
| | - Maureen A Sartor
- Correspondence address. Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, USA. Tel: +734-647-3155; Fax: +734-936-7283; E-mail: (D.C.D.); Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI 48109-2218, USA . Tel: +734-763-8013; Fax: +734-615-6553; E-mail: (M.A.S.)
| |
Collapse
|
124
|
Han Y, Nikolić M, Gobs M, Franzen J, de Haan G, Geiger H, Wagner W. Targeted methods for epigenetic age predictions in mice. Sci Rep 2020; 10:22439. [PMID: 33384442 PMCID: PMC7775437 DOI: 10.1038/s41598-020-79509-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Age-associated DNA methylation reflects aspect of biological aging—therefore epigenetic clocks for mice can elucidate how the aging process in this model organism is affected by specific treatments or genetic background. Initially, age-predictors for mice were trained for genome-wide DNA methylation profiles and we have recently described a targeted assay based on pyrosequencing of DNA methylation at only three age-associated genomic regions. Here, we established alternative approaches using droplet digital PCR (ddPCR) and barcoded bisulfite amplicon sequencing (BBA-seq). At individual CG dinucleotides (CpGs) the correlation of DNA methylation with chronological age was slightly higher for pyrosequencing and ddPCR as compared to BBA-seq. On the other hand, BBA-seq revealed that neighboring CpGs tend to be stochastically modified at murine age-associated regions. Furthermore, the binary sequel of methylated and non-methylated CpGs in individual reads can be used for single-read predictions, which may reflect heterogeneity in epigenetic aging. In comparison to C57BL/6 mice the single-read age-predictions using BBA-seq were also accelerated in the shorter-lived DBA/2 mice, and in C57BL/6 mice with a lifespan quantitative trait locus of DBA/2 mice. Taken together, we describe alternative targeted methods for epigenetic age predictions that provide new perspectives for aging-intervention studies in mice.
Collapse
Affiliation(s)
- Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Michael Gobs
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Gerald de Haan
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, the Netherlands
| | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, 89081, Ulm, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany.
| |
Collapse
|
125
|
Lu Y, Brommer B, Tian X, Krishnan A, Meer M, Wang C, Vera DL, Zeng Q, Yu D, Bonkowski MS, Yang JH, Zhou S, Hoffmann EM, Karg MM, Schultz MB, Kane AE, Davidsohn N, Korobkina E, Chwalek K, Rajman LA, Church GM, Hochedlinger K, Gladyshev VN, Horvath S, Levine ME, Gregory-Ksander MS, Ksander BR, He Z, Sinclair DA. Reprogramming to recover youthful epigenetic information and restore vision. Nature 2020; 588:124-129. [PMID: 33268865 PMCID: PMC7752134 DOI: 10.1038/s41586-020-2975-4] [Citation(s) in RCA: 345] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/22/2020] [Indexed: 02/07/2023]
Abstract
Ageing is a degenerative process that leads to tissue dysfunction and death. A proposed cause of ageing is the accumulation of epigenetic noise that disrupts gene expression patterns, leading to decreases in tissue function and regenerative capacity1-3. Changes to DNA methylation patterns over time form the basis of ageing clocks4, but whether older individuals retain the information needed to restore these patterns-and, if so, whether this could improve tissue function-is not known. Over time, the central nervous system (CNS) loses function and regenerative capacity5-7. Using the eye as a model CNS tissue, here we show that ectopic expression of Oct4 (also known as Pou5f1), Sox2 and Klf4 genes (OSK) in mouse retinal ganglion cells restores youthful DNA methylation patterns and transcriptomes, promotes axon regeneration after injury, and reverses vision loss in a mouse model of glaucoma and in aged mice. The beneficial effects of OSK-induced reprogramming in axon regeneration and vision require the DNA demethylases TET1 and TET2. These data indicate that mammalian tissues retain a record of youthful epigenetic information-encoded in part by DNA methylation-that can be accessed to improve tissue function and promote regeneration in vivo.
Collapse
Affiliation(s)
- Yuancheng Lu
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Benedikt Brommer
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Xiao Tian
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Anitha Krishnan
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Margarita Meer
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Chen Wang
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Daniel L Vera
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Qiurui Zeng
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Doudou Yu
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Michael S Bonkowski
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Jae-Hyun Yang
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Songlin Zhou
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Emma M Hoffmann
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Margarete M Karg
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Michael B Schultz
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Alice E Kane
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Noah Davidsohn
- Department of Genetics, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ekaterina Korobkina
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Karolina Chwalek
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Luis A Rajman
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - George M Church
- Department of Genetics, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Morgan E Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Meredith S Gregory-Ksander
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Bruce R Ksander
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Zhigang He
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - David A Sinclair
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA.
- Laboratory for Ageing Research, Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, New South Wales, Australia.
| |
Collapse
|
126
|
Levine M, McDevitt RA, Meer M, Perdue K, Di Francesco A, Meade T, Farrell C, Thrush K, Wang M, Dunn C, Pellegrini M, de Cabo R, Ferrucci L. A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin. eLife 2020; 9:e59201. [PMID: 33179594 PMCID: PMC7661040 DOI: 10.7554/elife.59201] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Robust biomarkers of aging have been developed from DNA methylation in humans and more recently, in mice. This study aimed to generate a novel epigenetic clock in rats-a model with unique physical, physiological, and biochemical advantages-by incorporating behavioral data, unsupervised machine learning, and network analysis to identify epigenetic signals that not only track with age, but also relates to phenotypic aging. Reduced representation bisulfite sequencing (RRBS) data was used to train an epigenetic age (DNAmAge) measure in Fischer 344 CDF (F344) rats. This measure correlated with age at (r = 0.93) in an independent sample, and related to physical functioning (p=5.9e-3), after adjusting for age and cell counts. DNAmAge was also found to correlate with age in male C57BL/6 mice (r = 0.79), and was decreased in response to caloric restriction. Our signatures driven by CpGs in intergenic regions that showed substantial overlap with H3K9me3, H3K27me3, and E2F1 transcriptional factor binding.
Collapse
Affiliation(s)
- Morgan Levine
- Department of Pathology, Yale University School of MedicineNew HavenUnited States
- Program in Computational Biology and Bioinformatics, Yale UniversityNew HavenUnited States
| | - Ross A McDevitt
- Comparative Medicine Section, Biomedical Research Center, National Institute on Aging, National Institutes of HealthBaltimoreUnited States
| | - Margarita Meer
- Department of Pathology, Yale University School of MedicineNew HavenUnited States
| | - Kathy Perdue
- Comparative Medicine Section, Biomedical Research Center, National Institute on Aging, National Institutes of HealthBaltimoreUnited States
| | - Andrea Di Francesco
- Translational Gerontology Branch, Biomedical Research Center, National Institute on Aging, National Institutes of HealthBaltimoreUnited States
- Calico Life SciencesSouth San FranciscoUnited States
| | - Theresa Meade
- Comparative Medicine Section, Biomedical Research Center, National Institute on Aging, National Institutes of HealthBaltimoreUnited States
| | - Colin Farrell
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
| | - Kyra Thrush
- Program in Computational Biology and Bioinformatics, Yale UniversityNew HavenUnited States
| | - Meng Wang
- Program in Computational Biology and Bioinformatics, Yale UniversityNew HavenUnited States
| | - Christopher Dunn
- Laboratory of Molecular Biology and Immunology, Flow Core Unit, Biomedical Research Center, National Institute on Aging, National Institutes of HealthBaltimoreUnited States
| | - Matteo Pellegrini
- Molecular Biology Institute and Departments of Energy Laboratory of Structural Biology and Molecular Medicine, and Chemistry and Biochemistry, University of California, Los AngelesLos AngelesUnited States
| | - Rafael de Cabo
- Translational Gerontology Branch, Biomedical Research Center, National Institute on Aging, National Institutes of HealthBaltimoreUnited States
| | - Luigi Ferrucci
- Translational Gerontology Branch, Biomedical Research Center, National Institute on Aging, National Institutes of HealthBaltimoreUnited States
| |
Collapse
|
127
|
He X, Liu J, Liu B, Shi J. The use of DNA methylation clock in aging research. Exp Biol Med (Maywood) 2020; 246:436-446. [PMID: 33175612 DOI: 10.1177/1535370220968802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
One of the key characteristics of aging is a progressive loss of physiological integrity, which weakens bodily functions and increases the risk of death. A robust biomarker is important for the assessment of biological age, the rate of aging, and a person's health status. DNA methylation clocks, novel biomarkers of aging, are composed of a group of cytosine-phosphate-guanine dinucleotides, the DNA methylation status of which can be used to accurately measure subjective age. These clocks are considered accurate biomarkers of chronological age for humans and other vertebrates. Numerous studies have demonstrated these clocks to quantify the rate of biological aging and the effects of longevity and anti-aging interventions. In this review, we describe the purpose and use of DNA methylation clocks in aging research.
Collapse
Affiliation(s)
- Xi He
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| | - Jiaojiao Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| | - Bo Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| |
Collapse
|
128
|
Roels J, Thénoz M, Szarzyńska B, Landfors M, De Coninck S, Demoen L, Provez L, Kuchmiy A, Strubbe S, Reunes L, Pieters T, Matthijssens F, Van Loocke W, Erarslan-Uysal B, Richter-Pechańska P, Declerck K, Lammens T, De Moerloose B, Deforce D, Van Nieuwerburgh F, Cheung LC, Kotecha RS, Mansour MR, Ghesquière B, Van Camp G, Berghe WV, Kowalczyk JR, Szczepański T, Davé UP, Kulozik AE, Goossens S, Curtis DJ, Taghon T, Dawidowska M, Degerman S, Van Vlierberghe P. Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia. Blood Cancer Discov 2020; 1:274-289. [PMID: 33179015 PMCID: PMC7116343 DOI: 10.1158/2643-3230.bcd-20-0059] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
Cancer cells display DNA hypermethylation at specific CpG islands in comparison to their normal healthy counterparts, but the mechanism that drives this so-called CpG island methylator phenotype (CIMP) remains poorly understood. Here, we show that CpG island methylation in human T-cell acute lymphoblastic leukemia (T-ALL) mainly occurs at promoters of Polycomb Repressor Complex 2 (PRC2) target genes that are not expressed in normal or malignant T-cells and which display a reciprocal association with H3K27me3 binding. In addition, we revealed that this aberrant methylation profile reflects the epigenetic history of T-ALL and is established already in pre-leukemic, self-renewing thymocytes that precede T-ALL development. Finally, we unexpectedly uncover that this age-related CpG island hypermethylation signature in T-ALL is completely resistant to the FDA-approved hypomethylating agent Decitabine. Altogether, we here provide conceptual evidence for the involvement of a pre-leukemic phase characterized by self-renewing thymocytes in the pathogenesis of human T-ALL.
Collapse
Affiliation(s)
- Juliette Roels
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Morgan Thénoz
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Mattias Landfors
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Stien De Coninck
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lisa Demoen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lien Provez
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Lindy Reunes
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Filip Matthijssens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Büşra Erarslan-Uysal
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Paulina Richter-Pechańska
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES) and Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara De Moerloose
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Laurence C Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia
| | - Rishi S Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia
| | - Marc R Mansour
- Department of Haematology, University College London Cancer Institute, London, England
| | - Bart Ghesquière
- Metabolomics Expertise Center, VIB Center for Cancer Biology, Leuven, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES) and Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Tomasz Szczepański
- Department of Pediatric Hematology and Oncology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Utpal P Davé
- Roudebush Veterans Affairs Medical Center and Indiana University School of Medicine, Indianapolis, Indiana
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - David J Curtis
- Australian Centre for Blood Diseases (ACBD), Monash University, Melbourne, Australia
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Sofie Degerman
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| |
Collapse
|
129
|
Coninx E, Chew YC, Yang X, Guo W, Coolkens A, Baatout S, Moons L, Verslegers M, Quintens R. Hippocampal and cortical tissue-specific epigenetic clocks indicate an increased epigenetic age in a mouse model for Alzheimer's disease. Aging (Albany NY) 2020; 12:20817-20834. [PMID: 33082299 PMCID: PMC7655172 DOI: 10.18632/aging.104056] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 04/17/2023]
Abstract
Epigenetic clocks are based on age-associated changes in DNA methylation of CpG-sites, which can accurately measure chronological age in different species. Recently, several studies have indicated that the difference between chronological and epigenetic age, defined as the age acceleration, could reflect biological age indicating functional decline and age-associated diseases. In humans, an epigenetic clock associated Alzheimer's disease (AD) pathology with an acceleration of the epigenetic age. In this study, we developed and validated two mouse brain region-specific epigenetic clocks from the C57BL/6J hippocampus and cerebral cortex. Both clocks, which could successfully estimate chronological age, were further validated in a widely used mouse model for AD, the triple transgenic AD (3xTg-AD) mouse. We observed an epigenetic age acceleration indicating an increased biological age for the 3xTg-AD mice compared to non-pathological C57BL/6J mice, which was more pronounced in the cortex as compared to the hippocampus. Genomic region enrichment analysis revealed that age-dependent CpGs were enriched in genes related to developmental, aging-related, neuronal and neurodegenerative functions. Due to the limited access of human brain tissues, these epigenetic clocks specific for mouse cortex and hippocampus might be important in further unravelling the role of epigenetic mechanisms underlying AD pathology or brain aging in general.
Collapse
Affiliation(s)
- Emma Coninx
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Yap Ching Chew
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Xiaojing Yang
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Wei Guo
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Amelie Coolkens
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Lieve Moons
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Roel Quintens
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| |
Collapse
|
130
|
Hoevenaar M, Goossens D, Roorda J. Angiotensin-converting enzyme 2, the complement system, the kallikrein-kinin system, type-2 diabetes, interleukin-6, and their interactions regarding the complex COVID-19 pathophysiological crossroads. J Renin Angiotensin Aldosterone Syst 2020; 21:1470320320979097. [PMID: 33283602 PMCID: PMC7724427 DOI: 10.1177/1470320320979097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022] Open
Abstract
Because of the current COVID-19-pandemic, the world is currently being held hostage in various lockdowns. ACE2 facilitates SARS-CoV-2 cell-entry, and is at the very center of several pathophysiological pathways regarding the RAAS, CS, KKS, T2DM, and IL-6. Their interactions with severe COVID-19 complications (e.g. ARDS and thrombosis), and potential therapeutic targets for pharmacological intervention, will be reviewed.
Collapse
Affiliation(s)
| | | | - Janne Roorda
- Medical Doctor, General Practice
van Dijk, Oisterwijk, The Netherlands
| |
Collapse
|
131
|
Kinzina ED, Podolskiy DI, Dmitriev SE, Gladyshev VN. Patterns of Aging Biomarkers, Mortality, and Damaging Mutations Illuminate the Beginning of Aging and Causes of Early-Life Mortality. Cell Rep 2020; 29:4276-4284.e3. [PMID: 31875539 DOI: 10.1016/j.celrep.2019.11.091] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/04/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022] Open
Abstract
An increase in the probability of death has been a defining feature of aging, yet human perinatal mortality starts high and decreases with age. Previous evolutionary models suggested that organismal aging begins after the onset of reproduction. However, we find that mortality and incidence of diseases associated with aging follow a U-shaped curve with the minimum before puberty, whereas quantitative biomarkers of aging, including somatic mutations and DNA methylation, do not, revealing that aging starts early but is masked by early-life mortality. Moreover, our genetic analyses point to the contribution of damaging mutations to early mortality. We propose that mortality patterns are governed, in part, by negative selection against damaging mutations in early life, manifesting after the corresponding genes are first expressed. Deconvolution of mortality patterns suggests that deleterious changes rather than mortality are the defining characteristic of aging and that aging begins in very early life.
Collapse
Affiliation(s)
- Elvira D Kinzina
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dmitriy I Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
132
|
Gladyshev VN. The Ground Zero of Organismal Life and Aging. Trends Mol Med 2020; 27:11-19. [PMID: 32980264 DOI: 10.1016/j.molmed.2020.08.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023]
Abstract
Cells may naturally proceed or be forced to transition to a state with a radically lower biological age, that is, be rejuvenated. Examples are the conversion of somatic cells to induced pluripotent stem cells and rejuvenation of the germline with each generation. We posit that these processes converge to the same 'ground zero', the mid-embryonic state characterized by the lowest biological age where both organismal life and aging begin. It may also be related to the phylotypic state. The ground zero model clarifies the relationship between aging, development, rejuvenation, and de-differentiation, which are distinct throughout life. By extending the rejuvenation phase during early embryogenesis and editing the genome, it may be possible to achieve the biological age at the ground zero lower than that achieved naturally.
Collapse
Affiliation(s)
- Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
133
|
Mitina M, Young S, Zhavoronkov A. Psychological aging, depression, and well-being. Aging (Albany NY) 2020; 12:18765-18777. [PMID: 32950973 PMCID: PMC7585090 DOI: 10.18632/aging.103880] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/25/2020] [Indexed: 01/24/2023]
Abstract
Aging is a multifactorial process, which affects the human body on every level and results in both biological and psychological changes. Multiple studies have demonstrated that a lower subjective age is associated with better mental and physical health, cognitive functions, well-being and satisfaction with life. In this work we propose a list of non-modifiable and modifiable factors that may possibly be influenced by subjective age and its changes across an individual's lifespan. These factors can be used for a future development of individual psychological aging clocks, which may be utilized as a sensitive measure for health status and overall life satisfaction. Furthermore, recent progress in artificial intelligence and biomarkers of biological aging have enabled scientists to discover and evaluate the efficacy of potential aging- and disease-modifying drugs and interventions. We propose that biomarkers of psychological age, which are just as important as those for biological age, may likewise be used for these purposes. Indeed, these two types of markers complement one another. We foresee the development of a broad range of parametric and deep psychological and biopsychological aging clocks, which may have implications for drug development and therapeutic interventions, and thus healthcare and other industries.
Collapse
Affiliation(s)
- Maria Mitina
- Deep Longevity, Inc., Three Exchange Square, The Landmark, Hong Kong, China
| | | | - Alex Zhavoronkov
- Deep Longevity, Inc., Three Exchange Square, The Landmark, Hong Kong, China,Insilico Medicine, Hong Kong Science and Technology Park (HKSTP), Hong Kong, China,The Buck Institute for Research on Aging, Novato, CA 94945, USA
| |
Collapse
|
134
|
Schultz MB, Kane AE, Mitchell SJ, MacArthur MR, Warner E, Vogel DS, Mitchell JR, Howlett SE, Bonkowski MS, Sinclair DA. Age and life expectancy clocks based on machine learning analysis of mouse frailty. Nat Commun 2020; 11:4618. [PMID: 32934233 PMCID: PMC7492249 DOI: 10.1038/s41467-020-18446-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/16/2020] [Indexed: 12/15/2022] Open
Abstract
The identification of genes and interventions that slow or reverse aging is hampered by the lack of non-invasive metrics that can predict the life expectancy of pre-clinical models. Frailty Indices (FIs) in mice are composite measures of health that are cost-effective and non-invasive, but whether they can accurately predict health and lifespan is not known. Here, mouse FIs are scored longitudinally until death and machine learning is employed to develop two clocks. A random forest regression is trained on FI components for chronological age to generate the FRIGHT (Frailty Inferred Geriatric Health Timeline) clock, a strong predictor of chronological age. A second model is trained on remaining lifespan to generate the AFRAID (Analysis of Frailty and Death) clock, which accurately predicts life expectancy and the efficacy of a lifespan-extending intervention up to a year in advance. Adoption of these clocks should accelerate the identification of longevity genes and aging interventions.
Collapse
Affiliation(s)
- Michael B Schultz
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Alice E Kane
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Sarah J Mitchell
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michael R MacArthur
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Elisa Warner
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - David S Vogel
- Voloridge Investment Management, LLC and VoLo Foundation, Jupiter, FL, USA
| | - James R Mitchell
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Susan E Howlett
- Departments of Pharmacology and Medicine (Geriatric Medicine), Dalhousie University, Halifax, NS, Canada
| | - Michael S Bonkowski
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
- Department of Dermatology, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David A Sinclair
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA.
- Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW, Australia.
| |
Collapse
|
135
|
Klosa J, Simon N, Westermark PO, Liebscher V, Wittenburg D. Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent. BMC Bioinformatics 2020; 21:407. [PMID: 32933477 PMCID: PMC7493359 DOI: 10.1186/s12859-020-03725-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/31/2020] [Indexed: 11/15/2022] Open
Abstract
Background Statistical analyses of biological problems in life sciences often lead to high-dimensional linear models. To solve the corresponding system of equations, penalization approaches are often the methods of choice. They are especially useful in case of multicollinearity, which appears if the number of explanatory variables exceeds the number of observations or for some biological reason. Then, the model goodness of fit is penalized by some suitable function of interest. Prominent examples are the lasso, group lasso and sparse-group lasso. Here, we offer a fast and numerically cheap implementation of these operators via proximal gradient descent. The grid search for the penalty parameter is realized by warm starts. The step size between consecutive iterations is determined with backtracking line search. Finally, seagull -the R package presented here- produces complete regularization paths. Results Publicly available high-dimensional methylation data are used to compare seagull to the established R package SGL. The results of both packages enabled a precise prediction of biological age from DNA methylation status. But even though the results of seagull and SGL were very similar (R2 > 0.99), seagull computed the solution in a fraction of the time needed by SGL. Additionally, seagull enables the incorporation of weights for each penalized feature. Conclusions The following operators for linear regression models are available in seagull: lasso, group lasso, sparse-group lasso and Integrative LASSO with Penalty Factors (IPF-lasso). Thus, seagull is a convenient envelope of lasso variants.
Collapse
Affiliation(s)
- Jan Klosa
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Germany
| | - Noah Simon
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Pål Olof Westermark
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Germany
| | - Volkmar Liebscher
- Institute of Mathematics and Computer Science, University of Greifswald, 17489, Greifswald, Germany
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Germany.
| |
Collapse
|
136
|
Osborne B, Bakula D, Ben Ezra M, Dresen C, Hartmann E, Kristensen SM, Mkrtchyan GV, Nielsen MH, Petr MA, Scheibye-Knudsen M. New methodologies in ageing research. Ageing Res Rev 2020; 62:101094. [PMID: 32512174 DOI: 10.1016/j.arr.2020.101094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/14/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023]
Abstract
Ageing is arguably the most complex phenotype that occurs in humans. To understand and treat ageing as well as associated diseases, highly specialised technologies are emerging that reveal critical insight into the underlying mechanisms and provide new hope for previously untreated diseases. Herein, we describe the latest developments in cutting edge technologies applied across the field of ageing research. We cover emerging model organisms, high-throughput methodologies and machine-driven approaches. In all, this review will give you a glimpse of what will be pushing the field onwards and upwards.
Collapse
Affiliation(s)
- Brenna Osborne
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Daniela Bakula
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Michael Ben Ezra
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Dresen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Esben Hartmann
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Stella M Kristensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Garik V Mkrtchyan
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Malte H Nielsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Michael A Petr
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
137
|
Sandoval‐Sierra JV, Helbing AHB, Williams EG, Ashbrook DG, Roy S, Williams RW, Mozhui K. Body weight and high-fat diet are associated with epigenetic aging in female members of the BXD murine family. Aging Cell 2020; 19:e13207. [PMID: 32790008 PMCID: PMC7511861 DOI: 10.1111/acel.13207] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/03/2020] [Accepted: 07/03/2020] [Indexed: 01/23/2023] Open
Abstract
DNA methylation (DNAm) is shaped by genetic and environmental factors and modulated by aging. Here, we examine interrelations between epigenetic aging, body weight (BW), and life span in 12 isogenic strains from the BXD family of mice that exhibit over twofold variation in longevity. Genome-wide DNAm was assayed in 70 liver specimens from predominantly female cases, 6-25 months old, that were maintained on normal chow or high-fat diet (HFD). We defined subsets of CpG regions associated with age, BW at young adulthood, and strain-by-diet-dependent life span. These age-associated differentially methylated CpG regions (age-DMRs) featured distinct genomic characteristics, with DNAm gains over time occurring in sites such as promoters and exons that have high CpG density and low average methylation. CpG regions associated with BW were enriched in introns, tended to have lower methylation in mice with higher BW, and were inversely correlated with gene expression (i.e., higher mRNA levels in mice with higher BW). CpG regions associated with life span were linked to genes involved in life span modulation, including the telomerase reverse transcriptase gene, Tert, which had both lower methylation and higher expression in long-lived strains. An epigenetic clock defined from age-DMRs revealed accelerated aging in mice belonging to strains with shorter life spans. Both higher BW and the HFD were associated with accelerated epigenetic aging. Our results highlight the age-accelerating effect of heavier BW. Furthermore, we demonstrate that the measure of epigenetic aging derived from age-DMRs can predict genotype and diet-induced differences in life span among female BXD members.
Collapse
Affiliation(s)
| | - Alexandra H. B. Helbing
- Department of Preventive Medicine University of Tennessee Health Science Center College of Medicine Memphis TN USA
| | - Evan G. Williams
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - David G. Ashbrook
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center College of Medicine Memphis TN USA
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center College of Medicine Memphis TN USA
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center College of Medicine Memphis TN USA
| | - Khyobeni Mozhui
- Department of Preventive Medicine University of Tennessee Health Science Center College of Medicine Memphis TN USA
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center College of Medicine Memphis TN USA
| |
Collapse
|
138
|
Zhang B, Gladyshev VN. How can aging be reversed? Exploring rejuvenation from a damage-based perspective. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10025. [PMID: 36619246 PMCID: PMC9744548 DOI: 10.1002/ggn2.10025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 01/11/2023]
Abstract
Advanced age is associated with accumulation of damage and other deleterious changes and a consequential systemic decline of function. This decline affects all organs and systems in an organism, leading to their inadaptability to the environment, and therefore is thought to be inevitable for humans and most animal species. However, in vitro and in vivo application of reprogramming strategies, which convert somatic cells to induced pluripotent stem cells, has demonstrated that the aged cells can be rejuvenated. Moreover, the data and theoretical considerations suggest that reversing the biological age of somatic cells (from old to young) and de-differentiating somatic cells into stem cells represent two distinct processes that take place during rejuvenation, and thus they may be differently targeted. We advance a stemness-function model to explain these data and discuss a possibility of rejuvenation from the perspective of damage accumulation. In turn, this suggests approaches to achieve rejuvenation of cells in vitro and in vivo.
Collapse
Affiliation(s)
- Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| |
Collapse
|
139
|
Tsurumi A, Li WX. Aging mechanisms-A perspective mostly from Drosophila. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10026. [PMID: 36619249 PMCID: PMC9744567 DOI: 10.1002/ggn2.10026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 01/11/2023]
Abstract
A mechanistic understanding of the natural aging process, which is distinct from aging-related disease mechanisms, is essential for developing interventions to extend lifespan or healthspan. Here, we discuss current trends in aging research and address conceptual and experimental challenges in the field. We examine various molecular markers implicated in aging with an emphasis on the role of heterochromatin and epigenetic changes. Studies in model organisms have been advantageous in elucidating conserved genetic and epigenetic mechanisms and assessing interventions that affect aging. We highlight the use of Drosophila, which allows controlled studies for evaluating genetic and environmental contributors to aging conveniently. Finally, we propose the use of novel methodologies and future strategies using Drosophila in aging research.
Collapse
Affiliation(s)
- Amy Tsurumi
- Department of SurgeryMassachusetts General Hospital, and Harvard Medical SchoolBostonMassachusettsUSA,Department of Microbiology and ImmunologyHarvard Medical SchoolBostonMassachusettsUSA,Shriners Hospitals for Children‐Boston®BostonMassachusettsUSA
| | - Willis X. Li
- Department of MedicineUniversity of California at San DiegoLa JollaCaliforniaUSA
| |
Collapse
|
140
|
Bergsma T, Rogaeva E. DNA Methylation Clocks and Their Predictive Capacity for Aging Phenotypes and Healthspan. Neurosci Insights 2020; 15:2633105520942221. [PMID: 32743556 PMCID: PMC7376380 DOI: 10.1177/2633105520942221] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
The number of age predictors based on DNA methylation (DNAm) profile is rising
due to their potential in predicting healthspan and application in age-related
illnesses, such as neurodegenerative diseases. The cumulative assessment of DNAm
levels at age-related CpGs (DNAm clock) may reflect biological aging. Such DNAm
clocks have been developed using various training models and could mirror
different aspects of disease/aging mechanisms. Hence, evaluating several DNAm
clocks together may be the most effective strategy in capturing the complexity
of the aging process. However, various confounders may influence the outcome of
these age predictors, including genetic and environmental factors, as well as
technical differences in the selected DNAm arrays. These factors should be taken
into consideration when interpreting DNAm clock predictions. In the current
review, we discuss 15 reported DNAm clocks with consideration for their utility
in investigating neurodegenerative diseases and suggest research directions
towards developing a more optimal measure for biological aging.
Collapse
Affiliation(s)
- Tessa Bergsma
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
141
|
Wang T, Ma J, Hogan AN, Fong S, Licon K, Tsui B, Kreisberg JF, Adams PD, Carvunis AR, Bannasch DL, Ostrander EA, Ideker T. Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. Cell Syst 2020; 11:176-185.e6. [PMID: 32619550 DOI: 10.1016/j.cels.2020.06.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 03/16/2020] [Accepted: 06/09/2020] [Indexed: 12/21/2022]
Abstract
All mammals progress through similar physiological stages throughout life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects underlying genomic events is unclear. Here, we map the common methylation changes experienced by mammalian genomes as they age, focusing on comparison of humans with dogs, an emerging model of aging. Using oligo-capture sequencing, we characterize methylomes of 104 Labrador retrievers spanning a 16-year age range, achieving >150× coverage within mammalian syntenic blocks. Comparison with human methylomes reveals a nonlinear relationship that translates dog-to-human years and aligns the timing of major physiological milestones between the two species, with extension to mice. Conserved changes center on developmental gene networks, which are sufficient to translate age and the effects of anti-aging interventions across multiple mammals. These results establish methylation not only as a diagnostic age readout but also as a cross-species translator of physiological aging milestones.
Collapse
Affiliation(s)
- Tina Wang
- Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jianzhu Ma
- Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andrew N Hogan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samson Fong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Licon
- Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian Tsui
- Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason F Kreisberg
- Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, La Jolla, CA 92093, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
142
|
Cao L, Zhu T, Lang X, Jia S, Yang Y, Zhu C, Wang Y, Feng S, Wang C, Zhang P, Chen J, Jiang H. Inhibiting DNA Methylation Improves Survival in Severe Sepsis by Regulating NF-κB Pathway. Front Immunol 2020; 11:1360. [PMID: 32714333 PMCID: PMC7343767 DOI: 10.3389/fimmu.2020.01360] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
Organ dysfunction caused by sepsis is life-threatening and results in high mortality. Therapeutic options for sepsis are limited. Pathogenic factors are considered as components of environmental pressure that modify DNA methylation patterns thereby enhancing disease progression. Here, we found that sepsis patients exhibited higher levels of genomic DNA methylation patterns and hypermethylated genes associated with the NF-kB signaling pathway. Therefore, we hypothesized that a DNA methyl transferase inhibitor, Decitabine, may mitigate inflammation and improve survival by inhibiting the NF-κB signaling pathway. To test the hypothesis, mice challenged with caecal ligation and puncture (CLP) were subcutaneously injected with Decitabine solution (0.5, 1, and 1.5 mg/kg) 2 h following operation. Our results indicated that Decitabine reduces DNA methyltransferases (DNMTs), attenuates NF-κB activation, downregulates inflammatory cytokine levels, and inhibits the progression of sepsis. Thus, DNA methylation may be indispensable for sepsis and serve as a predicting factor. The use of Decitabine could represent a novel strategy in the treatment of sepsis.
Collapse
Affiliation(s)
- Luxi Cao
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Tingting Zhu
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Xiabing Lang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Sha Jia
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Yi Yang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Chaohong Zhu
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Yucheng Wang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Shi Feng
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Cuili Wang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Ping Zhang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Jianghua Chen
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Hong Jiang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| |
Collapse
|
143
|
Biohorology and biomarkers of aging: Current state-of-the-art, challenges and opportunities. Ageing Res Rev 2020; 60:101050. [PMID: 32272169 DOI: 10.1016/j.arr.2020.101050] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/06/2020] [Accepted: 03/22/2020] [Indexed: 02/08/2023]
Abstract
The aging process results in multiple traceable footprints, which can be quantified and used to estimate an organism's age. Examples of such aging biomarkers include epigenetic changes, telomere attrition, and alterations in gene expression and metabolite concentrations. More than a dozen aging clocks use molecular features to predict an organism's age, each of them utilizing different data types and training procedures. Here, we offer a detailed comparison of existing mouse and human aging clocks, discuss their technological limitations and the underlying machine learning algorithms. We also discuss promising future directions of research in biohorology - the science of measuring the passage of time in living systems. Overall, we expect deep learning, deep neural networks and generative approaches to be the next power tools in this timely and actively developing field.
Collapse
|
144
|
Multifaceted deregulation of gene expression and protein synthesis with age. Proc Natl Acad Sci U S A 2020; 117:15581-15590. [PMID: 32576685 DOI: 10.1073/pnas.2001788117] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein synthesis represents a major metabolic activity of the cell. However, how it is affected by aging and how this in turn impacts cell function remains largely unexplored. To address this question, herein we characterized age-related changes in both the transcriptome and translatome of mouse tissues over the entire life span. We showed that the transcriptome changes govern those in the translatome and are associated with altered expression of genes involved in inflammation, extracellular matrix, and lipid metabolism. We also identified genes that may serve as candidate biomarkers of aging. At the translational level, we uncovered sustained down-regulation of a set of 5'-terminal oligopyrimidine (5'-TOP) transcripts encoding protein synthesis and ribosome biogenesis machinery and regulated by the mTOR pathway. For many of them, ribosome occupancy dropped twofold or even more. Moreover, with age, ribosome coverage gradually decreased in the vicinity of start codons and increased near stop codons, revealing complex age-related changes in the translation process. Taken together, our results reveal systematic and multidimensional deregulation of protein synthesis, showing how this major cellular process declines with age.
Collapse
|
145
|
Brd2 haploinsufficiency extends lifespan and healthspan in C57B6/J mice. PLoS One 2020; 15:e0234910. [PMID: 32559200 PMCID: PMC7304595 DOI: 10.1371/journal.pone.0234910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/04/2020] [Indexed: 11/19/2022] Open
Abstract
Aging in mammals is the gradual decline of an organism's physical, mental, and physiological capacity. Aging leads to increased risk for disease and eventually to death. Here, we show that Brd2 haploinsufficiency (Brd2+/-) extends lifespan and increases healthspan in C57B6/J mice. In Brd2+/- mice, longevity is increased by 23% (p<0.0001), and, relative to wildtype animals (Brd2+/+), cancer incidence is reduced by 43% (p<0.001). In addition, relative to age-matched wildtype mice, Brd2 heterozygotes show healthier aging including: improved grooming, extended period of fertility, and lack of age-related decline in kidney function and morphology. Our data support a role for haploinsufficiency of Brd2 in promoting healthy aging. We hypothesize that Brd2 affects aging by protecting against the accumulation of molecular and cellular damage. Given the recent advances in the development of BET inhibitors, our research provides impetus to test drugs that target BRD2 as a way to understand and treat/prevent age-related diseases.
Collapse
|
146
|
Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissue. Aging (Albany NY) 2020; 12:12393-12409. [PMID: 32554863 PMCID: PMC7343460 DOI: 10.18632/aging.103499] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/01/2020] [Indexed: 01/05/2023]
Abstract
In recent years, reports of non-linear regulations in age- and longevity-associated biological processes have been accumulating. Inspired by methodological advances in precision medicine involving the integrative analysis of multi-omics data, we sought to investigate the potential of multi-omics integration to identify distinct stages in the aging progression from ex vivo human skin tissue. For this we generated transcriptome and methylome profiling data from suction blister lesions of female subjects between 21 and 76 years, which were integrated using a network fusion approach. Unsupervised cluster analysis on the combined network identified four distinct subgroupings exhibiting a significant age-association. As indicated by DNAm age analysis and Hallmark of Aging enrichment signals, the stages captured the biological aging state more clearly than a mere grouping by chronological age and could further be recovered in a longitudinal validation cohort with high stability. Characterization of the biological processes driving the phases using machine learning enabled a data-driven reconstruction of the order of Hallmark of Aging manifestation. Finally, we investigated non-linearities in the mid-life aging progression captured by the aging phases and identified a far-reaching non-linear increase in transcriptional noise in the pathway landscape in the transition from mid- to late-life.
Collapse
|
147
|
Metformin: Sentinel of the Epigenetic Landscapes That Underlie Cell Fate and Identity. Biomolecules 2020; 10:biom10050780. [PMID: 32443566 PMCID: PMC7277648 DOI: 10.3390/biom10050780] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/08/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
The biguanide metformin is the first drug to be tested as a gerotherapeutic in the clinical trial TAME (Targeting Aging with Metformin). The current consensus is that metformin exerts indirect pleiotropy on core metabolic hallmarks of aging, such as the insulin/insulin-like growth factor 1 and AMP-activated protein kinase/mammalian Target Of Rapamycin signaling pathways, downstream of its primary inhibitory effect on mitochondrial respiratory complex I. Alternatively, but not mutually exclusive, metformin can exert regulatory effects on components of the biologic machinery of aging itself such as chromatin-modifying enzymes. An integrative metabolo-epigenetic outlook supports a new model whereby metformin operates as a guardian of cell identity, capable of retarding cellular aging by preventing the loss of the information-theoretic nature of the epigenome. The ultimate anti-aging mechanism of metformin might involve the global preservation of the epigenome architecture, thereby ensuring cell fate commitment and phenotypic outcomes despite the challenging effects of aging noise. Metformin might therefore inspire the development of new gerotherapeutics capable of preserving the epigenome architecture for cell identity. Such gerotherapeutics should replicate the ability of metformin to halt the erosion of the epigenetic landscape, mitigate the loss of cell fate commitment, delay stochastic/environmental DNA methylation drifts, and alleviate cellular senescence. Yet, it remains a challenge to confirm if regulatory changes in higher-order genomic organizers can connect the capacity of metformin to dynamically regulate the three-dimensional nature of epigenetic landscapes with the 4th dimension, the aging time.
Collapse
|
148
|
Zhang B, Podolskiy DI, Mariotti M, Seravalli J, Gladyshev VN. Systematic age-, organ-, and diet-associated ionome remodeling and the development of ionomic aging clocks. Aging Cell 2020; 19:e13119. [PMID: 32323920 PMCID: PMC7253066 DOI: 10.1111/acel.13119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/28/2019] [Accepted: 01/25/2020] [Indexed: 12/13/2022] Open
Abstract
Aging involves coordinated yet distinct changes in organs and systems throughout life, including changes in essential trace elements. However, how aging affects tissue element composition (ionome) and how these changes lead to dysfunction and disease remain unclear. Here, we quantified changes in the ionome across eight organs and 16 age groups of mice. This global profiling revealed novel interactions between elements at the level of tissue, age, and diet, and allowed us to achieve a broader, organismal view of the aging process. We found that while the entire ionome steadily transitions along the young-to-old trajectory, individual organs are characterized by distinct element changes. The ionome of mice on calorie restriction (CR) moved along a similar but shifted trajectory, pointing that at the organismal level this dietary regimen changes metabolism in order to slow down aging. However, in some tissues CR mimicked a younger state of control mice. Even though some elements changed with age differently in different tissues, in general aging was characterized by the reduced levels of elements as well as their increased variance. The dataset we prepared also allowed to develop organ-specific, ionome-based markers of aging that could help monitor the rate of aging. In some tissues, these markers reported the lifespan-extending effect of CR. These aging biomarkers have the potential to become an accessible tool to test the age-modulating effects of interventions.
Collapse
Affiliation(s)
- Bohan Zhang
- Division of GeneticsDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| | - Dmitriy I. Podolskiy
- Division of GeneticsDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| | - Marco Mariotti
- Division of GeneticsDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| | - Javier Seravalli
- Redox Biology Center and Department of BiochemistryUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Vadim N. Gladyshev
- Division of GeneticsDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| |
Collapse
|
149
|
Braga DL, Mousovich-Neto F, Tonon-da-Silva G, Salgueiro WG, Mori MA. Epigenetic changes during ageing and their underlying mechanisms. Biogerontology 2020; 21:423-443. [PMID: 32356238 DOI: 10.1007/s10522-020-09874-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022]
Abstract
As life expectancy increases worldwide, ageing and age-related diseases arise as a major issue for societies around the globe. Understanding the biological mechanisms underlying the ageing process is thus instrumental for the development of efficient interventions aimed to prevent and treat age-related conditions. Current knowledge in the biogerontology field points to epigenetics as a critical component of the ageing process, not only by serving as a bona-fide marker of biological age but also by controlling and conferring inheritability to cellular and organismal ageing. This is reflected by a myriad of evidences demonstrating the relationship between DNA methylation, histone modifications, chromatin remodeling and small non-coding RNAs and several age-related phenotypes. Given the reversibility of epigenetic alterations, epigenetic reprogramming may also be envisioned as a potential approach to treat age-related disorders. Here we review how different types of epigenetic mechanisms are involved in the ageing process. In addition, we highlight how interventions modulate epigenetics and thus promote health- and lifespan.
Collapse
Affiliation(s)
- Deisi L Braga
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Felippe Mousovich-Neto
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
| | - Guilherme Tonon-da-Silva
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Willian G Salgueiro
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil.
- Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, São Paulo, 13083-862, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, São Paulo, 13083-862, Brazil.
| |
Collapse
|
150
|
Raj K, Horvath S. Current perspectives on the cellular and molecular features of epigenetic ageing. Exp Biol Med (Maywood) 2020; 245:1532-1542. [PMID: 32276545 DOI: 10.1177/1535370220918329] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IMPACT STATEMENT The field of epigenetic ageing is relatively new, and the speed of its expansion presents a challenge in keeping abreast with new discoveries and their implications. Several reviews have already addressed the great number of pathologies, health conditions, life-style, and external stressors that are associated with changes to the rate of epigenetic ageing. While these associations highlight and affirm the ability of epigenetic clock to capture biologically meaningful changes associated with age, they do not inform us about the underlying mechanisms. In this very early period since the development of the clock, there have been rather limited experimental research that are aimed at uncovering the mechanism. Hence, the perspective that we proffer is derived from available but nevertheless limited lines of evidence that together provide a seemingly coherent narrative that can be tested. This, we believe would be helpful towards uncovering the workings of the epigenetic clock.
Collapse
Affiliation(s)
- Kenneth Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA and Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, CA 90095, USA
| |
Collapse
|